[VPM] comments on this code?
nkuipers
nkuipers at uvic.ca
Tue Apr 1 17:45:22 CST 2003
Hello again,
I wrote earlier about using Perl to automate a script's recovery from
server-side troubles (the machine I am thinking of tends to crap out more than
the others, and needs to be rebooted). Peter directed me to perlipc, and from
reading about pipes and the like, I came up with the following. Please let me
know if I am doing anything BAD BAD BAD...
sub blast {
my $data = shift;
my $temp = "$ENV{HOME}/temp/seq.tmp";
my $fifo = "ssh snoopy.ceh.uvic.ca /usr/local/bin/blastall";
my @args = ('-p blastn', '-d nt', '-e 0.0000001', '-m 7');
### load input file with fasta-formatted queryid/sequence ###
open SEQ, ">$temp" or die "Could not open for write:$!";
print SEQ ">",$data->[0],"\n",$data->[1];
close SEQ;
### open a handle to BLAST output, retry if unsuccessful for any reason ###
{
if (!open BLAST, "$fifo @args <$temp|") {
#
print LOG "BLAST connection refused, retrying...\n";
#
sleep(300);
redo;
}
}
### process the report ###
parse(*BLAST);
}
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